1st Semester 71 - BIOLOGY JUNCTION

Chapter 25 AP Objectives

Chapter 25 Tracing Phylogeny

Objectives

Phylogenies are Based on Common Ancestries
1.	Distinguish between phylogeny and systematics.
2.	Describe the process of sedimentation and the formation of fossils. Explain which portions of organisms are most likely to fossilize.
3.	Explain why it is crucial to distinguish between homology and analogy before selecting characters to use in the reconstruction of phylogeny.
4.	Explain why bird and bat wings are homologous as vertebrate forelimbs but analogous as wings.
5.	Define molecular systematics. Explain some of the problems that systematists may face in carrying out molecular comparisons of nucleic acids.

	Phylogenetic Systematics: Connecting Classification with Evolutionary History
6.	Explain the following characteristics of the Linnaean system of classification: a. binomial nomenclature b. hierarchical classification
7.	List the major taxonomic categories from most to least inclusive.
8.	Define a clade. Distinguish between a monophyletic clade and paraphyletic and polyphyletic groupings of species.
9.	Distinguish between shared primitive characters and shared derived characters.
10.	Explain how shared derived characters can be used to construct a phylogenetic diagram.
11.	Explain how outgroup comparison can be used to distinguish between shared primitive characters and shared derived characters.
12.	Define an ingroup.
13.	Distinguish between a phylogram and an ultrameric tree.
14.	Discuss how systematists use the principles of maximum parsimony and maximum likelihood in reconstructing phylogenies.
15.	Explain why any phylogenetic diagram represents a hypothesis about evolutionary relationships among organisms.
16.	Distinguish between orthologous and paralogous genes. Explain how gene duplication has led to families of paralogous genes.
17.	Explain how molecular clocks are used to determine the approximate time of key evolutionary events. Explain how molecular clocks are calibrated in actual time.
18.	Describe some of the limitations of molecular clocks.
19.	Explain the neutral theory of evolutionary change.
20.	Explain how scientists determined the approximate time when HIV-1 M first infected humans.
21.	Describe the evidence that suggests there is a universal tree of life.

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Chapter 3 – Water and the Fitness of the Environment – Lecture Outline

Chapter 3 Water and the Fitness of the Environment Lecture Outline

Overview: The Molecule That Supports All of Life

Because water is the substance that makes life possible on Earth, astronomers hope to find evidence of water on newly discovered planets orbiting distant stars.
Life on Earth began in water and evolved there for 3 billion years before colonizing the land.
Even terrestrial organisms are tied to water.
Most cells are surrounded by water.
Cells are about 70–95% water.
Water is a reactant in many of the chemical reactions of life.
Water is the only common substance that exists in the natural world in all three physical states of matter: solid ice, liquid water, and water vapor.

Concept 3.1 The polarity of water molecules results in hydrogen bonding

In a water molecule, two hydrogen atoms form single polar covalent bonds with an oxygen atom.
Because oxygen is more electronegative than hydrogen, the region around the oxygen atom has a partial negative charge.
The regions near the two hydrogen atoms have a partial positive charge.
A water molecule is a polar molecule in which opposite ends of the molecule have opposite charges.
Water has a variety of unusual properties because of the attraction between polar water molecules.
The slightly negative regions of one water molecule are attracted to the slightly positive regions of nearby water molecules, forming hydrogen bonds.
Each water molecule can form hydrogen bonds with up to four neighbors.

Concept 3.2 Four emergent properties of water contribute to Earth’s fitness for life

Organisms depend on the cohesion of water molecules.
The hydrogen bonds joining water molecules are weak, about 1/20 as strong as covalent bonds.
They form, break, and reform with great frequency. Each hydrogen bond lasts only a few trillionths of a second.
At any instant, a substantial percentage of all water molecules are bonded to their neighbors, creating a high level of structure.
Collectively, hydrogen bonds hold water together, a phenomenon called cohesion.
Cohesion among water molecules plays a key role in the transport of water and dissolved nutrients against gravity in plants.
Water molecules move from the roots to the leaves of a plant through water-conducting vessels.
As water molecules evaporate from a leaf, other water molecules from vessels in the leaf replace them.
Hydrogen bonds cause water molecules leaving the vessels to tug on molecules farther down.
This upward pull is transmitted down to the roots.
Adhesion, clinging of one substance to another, contributes too, as water adheres to the wall of the vessels.
Surface tension, a measure of the force necessary to stretch or break the surface of a liquid, is related to cohesion.
Water has a greater surface tension than most other liquids because hydrogen bonds among surface water molecules resist stretching or breaking the surface.
Water behaves as if covered by an invisible film.
Some animals can stand, walk, or run on water without breaking the surface.
Water moderates temperatures on Earth.
Water stabilizes air temperatures by absorbing heat from warmer air and releasing heat to cooler air.
Water can absorb or release relatively large amounts of heat with only a slight change in its own temperature.
Atoms and molecules have kinetic energy, the energy of motion, because they are always moving.
The faster a molecule moves, the more kinetic energy it has.
Heat is a measure of the total quantity of kinetic energy due to molecular motion in a body of matter.
Temperature measures the intensity of heat in a body of matter due to the average kinetic energy of molecules.
As the average speed of molecules increases, a thermometer will record an increase in temperature.
Heat and temperature are related, but not identical.
When two objects of different temperatures come together, heat passes from the warmer object to the cooler object until the two are the same temperature.
Molecules in the cooler object speed up at the expense of kinetic energy of the warmer object.
Ice cubes cool a glass of pop by absorbing heat from the pop as the ice melts.
In most biological settings, temperature is measured on the Celsius scale (°C).
At sea level, water freezes at 0°C and boils at 100°C.
Human body temperature is typically 37°C.
While there are several ways to measure heat energy, one convenient unit is the calorie (cal).
One calorie is the amount of heat energy necessary to raise the temperature of one g of water by 1°C.
A calorie is released when 1 g of water cools by 1°C.
In many biological processes, the kilocalorie (kcal) is more convenient.
A kilocalorie is the amount of heat energy necessary to raise the temperature of 1000 g of water by 1°C.
Another common energy unit, the joule (J), is equivalent to 0.239 cal.
Water stabilizes temperature because it has a high specific heat.
The specific heat of a substance is the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1°C.
By definition, the specific heat of water is 1 cal per gram per degree Celsius or 1 cal/g/°C.
Water has a high specific heat compared to other substances.
For example, ethyl alcohol has a specific heat of 0.6 cal/g/°C.
The specific heat of iron is 1/10 that of water.
Water resists changes in temperature because of its high specific heat.
In other words, water absorbs or releases a relatively large quantity of heat for each degree of temperature change.
Water’s high specific heat is due to hydrogen bonding.
Heat must be absorbed to break hydrogen bonds, and heat is released when hydrogen bonds form.
Investment of one calorie of heat causes relatively little change to the temperature of water because much of the energy is used to disrupt hydrogen bonds, not speed up the movement of water molecules.
Water’s high specific heat has effects that range from the level of the whole Earth to the level of individual organisms.
A large body of water can absorb a large amount of heat from the sun in daytime during the summer and yet warm only a few degrees.
At night and during the winter, the warm water will warm cooler air.
Therefore, ocean temperatures and coastal land areas have more stable temperatures than inland areas.
Living things are made primarily of water. Consequently, they resist changes in temperature better than they would if composed of a liquid with a lower specific heat.
The transformation of a molecule from a liquid to a gas is called vaporization or evaporation.
This occurs when the molecule moves fast enough to overcome the attraction of other molecules in the liquid.
Even in a low-temperature liquid (with low average kinetic energy), some molecules are moving fast enough to evaporate.
Heating a liquid increases the average kinetic energy and increases the rate of evaporation.
Heat of vaporization is the quantity of heat that a liquid must absorb for 1 g of it to be converted from liquid to gas.
Water has a relatively high heat of vaporization, requiring about 580 cal of heat to evaporate 1 g of water at room temperature.
This is double the heat required to vaporize the same quantity of alcohol or ammonia.
This is because hydrogen bonds must be broken before a water molecule can evaporate from the liquid.
Water’s high heat of vaporization moderates climate.
Much of the sun’s heat absorbed by tropical oceans is used for evaporation of surface water.
As moist tropical air moves to the poles, water vapor condenses to form rain, releasing heat.
As a liquid evaporates, the surface of the liquid that remains behind cools, a phenomenon called evaporative cooling.
This occurs because the most energetic molecules are the most likely to evaporate, leaving the lower–kinetic energy molecules behind.
Evaporative cooling moderates temperature in lakes and ponds.
Evaporation of sweat in mammals or evaporation of water from the leaves of plants prevents terrestrial organisms from overheating.
Evaporation of water from the leaves of plants or the skin of humans removes excess heat.
Oceans and lakes don’t freeze solid because ice floats.
Water is unusual because it is less dense as a solid than as a cold liquid.
Most materials contract as they solidify, but water expands.
At temperatures above 4°C, water behaves like other liquids, expanding as it warms and contracting as it cools.
Water begins to freeze when its molecules are no longer moving vigorously enough to break their hydrogen bonds.
When water reaches 0°C, water becomes locked into a crystalline lattice, with each water molecule bonded to a maximum of four partners.
As ice starts to melt, some of the hydrogen bonds break, and water molecules can slip closer together than they can while in the ice state.
Ice is about 10% less dense than water at 4°C.
Therefore, ice floats on the cool water below.
This oddity has important consequences for life.
If ice sank, eventually all ponds, lakes, and even the ocean would freeze solid.
During the summer, only the upper few centimeters of the ocean would thaw.
Instead, the surface layer of ice insulates liquid water below, preventing it from freezing and allowing life to exist under the frozen surface.
Water is the solvent of life.
A liquid that is a completely homogeneous mixture of two or more substances is called a solution.
A sugar cube in a glass of water will eventually dissolve to form a uniform solution of sugar and water.
The dissolving agent is the solvent, and the substance that is dissolved is the solute.
In our example, water is the solvent and sugar is the solute.
In an aqueous solution, water is the solvent.
Water is not a universal solvent, but it is very versatile because of the polarity of water molecules.
° Water is an effective solvent because it readily forms hydrogen bonds with charged and polar covalent molecules.
° For example, when a crystal of salt (NaCl) is placed in water, the Na+ cations interact with the partial negative charges of the oxygen regions of water molecules.
° The Cl− anions interact with the partial positive charges of the hydrogen regions of water molecules.
· Each dissolved ion is surrounded by a sphere of water molecules, a hydration shell.
· Eventually, water dissolves all the ions, resulting in a solution with two solutes: sodium and chloride ions.
· Polar molecules are also soluble in water because they form hydrogen bonds with water.
· Even large molecules, like proteins, can dissolve in water if they have ionic and polar regions.
· Any substance that has an affinity for water is hydrophilic (water-loving).
° These substances are dominated by ionic or polar bonds.
· Some hydrophilic substances do not dissolve because their molecules are too large.
° For example, cotton is hydrophilic because cellulose, its major constituent, has numerous polar covalent bonds. However, its giant cellulose molecules are too large to dissolve in water.
° Water molecules form hydrogen bonds with the cellulose fibers of cotton, allowing you to dry yourself with your cotton towel as the water is pulled into the towel.
· Substances that have no affinity for water are hydrophobic (water-fearing).
° These substances are nonionic and have nonpolar covalent bonds.
° Because there are no consistent regions with partial or full charges, water molecules cannot form hydrogen bonds with hydrophobic molecules.
° Oils such as vegetable oil are hydrophobic because the dominant bonds, carbon-carbon and carbon-hydrogen, share electrons equally.
° Hydrophobic molecules are major ingredients of cell membranes.
· Biological chemistry is “wet” chemistry with most reactions involving solutes dissolved in water.
· Chemical reactions depend on collisions of molecules and therefore on the concentrations of solutes in aqueous solution.
· We measure the number of molecules in units called moles.
· The actual number of molecules in a mole is called Avogadro’s number, 6.02 × 1023.
· A mole is equal to the molecular weight of a substance but scaled up from daltons to grams.
· To illustrate, how could we measure out a mole of table sugar—sucrose (C12H22O11)?
° A carbon atom weighs 12 daltons, hydrogen 1 dalton, and oxygen 16 daltons.
° One molecule of sucrose would weigh 342 daltons, the sum of weights of all the atoms in sucrose, or the molecular weight of sucrose.
° To get one mole of sucrose, we would weigh out 342 g.
· The advantage of using moles as a measurement is that a mole of one substance has the same number of molecules as a mole of any other substance.
° If substance A has a molecular weight of 10 daltons and substance B has a molecular weight of 100 daltons, then we know that 10 g of substance A has the same number of molecules as 100 g of substance B.
° A mole of sucrose contains 6.02 × 1023 molecules and weighs 342 g, while a mole of ethyl alcohol (C2H6O) also contains 6.02 × 1023 molecules but weighs only 46 g because the molecules are smaller.
° Measuring in moles allows scientists to combine substances in fixed ratios of molecules.
· In “wet” chemistry, we are typically combining solutions or measuring the quantities of materials in aqueous solutions.
° The concentration of a material in solution is called its molarity.
° A one molar solution has one mole of a substance dissolved in one liter of solvent, typically water.
° To make a 1 molar (1M) solution of sucrose, we would slowly add water to 342 g of sucrose until the total volume was 1 liter and all the sugar was dissolved.

Concept 3.3 Dissociation of water molecules leads to acidic and basic conditions that affect living organisms

· Occasionally, a hydrogen atom participating in a hydrogen bond between two water molecules shifts from one molecule to the other.
° The hydrogen atom leaves its electron behind and is transferred as a single proton—a hydrogen ion (H+).
° The water molecule that lost the proton is now a hydroxide ion (OH−).
° The water molecule with the extra proton is now a hydronium ion (H3O+).
· A simplified way to view this process is to say that a water molecule dissociates into a hydrogen ion and a hydroxide ion:
° H2O <=> H+ + OH−
· This reaction is reversible.
· At equilibrium, the concentration of water molecules greatly exceeds that of H+ and OH−.
· In pure water, only one water molecule in every 554 million is dissociated.
° At equilibrium, the concentration of H+ or OH− is 10−7M (at 25°C).
· Although the dissociation of water is reversible and statistically rare, it is very important in the chemistry of life.
· Because hydrogen and hydroxide ions are very reactive, changes in their concentrations can drastically affect the chemistry of a cell.
· Adding certain solutes, called acids and bases, disrupts the equilibrium and modifies the concentrations of hydrogen and hydroxide ions.
· The pH scale is used to describe how acidic or basic a solution is.
Organisms are sensitive to changes in pH.
· An acid is a substance that increases the hydrogen ion concentration in a solution.
° When hydrochloric acid is added to water, hydrogen ions dissociate from chloride ions: HCl -> H+ + Cl−
° Addition of an acid makes a solution more acidic.
· Any substance that reduces the hydrogen ion concentration in a solution is a base.
· Some bases reduce the H+ concentration directly by accepting hydrogen ions.
° Ammonia (NH3) acts as a base when the nitrogen’s unshared electron pair attracts a hydrogen ion from the solution, creating an ammonium ion (NH4+).
° NH3 + H+ <=> NH4+
· Other bases reduce H+ indirectly by dissociating to OH−, which then combines with H+ to form water.
° NaOH -> Na+ + OH− OH− + H+ -> H2O
· Solutions with more OH− than H+ are basic solutions.
· Solutions with more H+ than OH− are acidic solutions.
· Solutions in which concentrations of OH− and H+ are equal are neutral solutions.
· Some acids and bases (HCl and NaOH) are strong acids or bases.
° These molecules dissociate completely in water.
· Other acids and bases (NH3) are weak acids or bases.
° For these molecules, the binding and release of hydrogen ions are reversible.
° At equilibrium, there will be a fixed ratio of products to reactants.
° Carbonic acid (H2CO3) is a weak acid:
§ H2CO3 <=> HCO3− + H+
§ At equilibrium, 1% of the H2CO3 molecules will be dissociated.
· In any solution, the product of the H+ and OH− concentrations is constant at 10−14.
· Brackets ([H+] and [OH−]) indicate the molar concentration of the enclosed substance.
° [H+] [OH−] = 10−14
° In a neutral solution, [H+] = 10−7 M and [OH−] = 10−7 M
· Adding acid to a solution shifts the balance between H+ and OH− toward H+ and leads to a decline in OH−.
° If [H+] = 10−5 M, then [OH−] = 10−9 M
° Hydroxide concentrations decline because some of the additional acid combines with hydroxide to form water.
· Adding a base does the opposite, increasing OH− concentration and lowering H+ concentration.
· The H+ and OH− concentrations of solutions can vary by a factor of 100 trillion or more.
· To express this variation more conveniently, the H+ and OH− concentrations are typically expressed via the pH scale.
° The pH scale, ranging from 1 to 14, compresses the range of concentrations by employing logarithms.
° pH = − log [H+] or [H+] = 10−pH
° In a neutral solution, [H+] = 10−7 M, and the pH = 7.
· Values for pH decline as [H+] increase.
· While the pH scale is based on [H+], values for [OH−] can be easily calculated from the product relationship.
· The pH of a neutral solution is 7.
· Acidic solutions have pH values less than 7, and basic solutions have pH values greater than 7.
· Most biological fluids have pH values in the range of 6 to 8.
° However, the human stomach has strongly acidic digestive juice with a pH of about 2.
· Each pH unit represents a tenfold difference in H+ and OH− concentrations.
° A small change in pH actually indicates a substantial change in H+ and OH− concentrations.
· The chemical processes in the cell can be disrupted by changes to the H+ and OH− concentrations away from their normal values, usually near pH 7.
· To maintain cellular pH values at a constant level, biological fluids have buffers.
· Buffers resist changes to the pH of a solution when H+ or OH− is added to the solution.
° Buffers accept hydrogen ions from the solution when they are in excess and donate hydrogen ions when they have been depleted.
° Buffers typically consist of a weak acid and its corresponding base.
° One important buffer in human blood and other biological solutions is carbonic acid, which dissociates to yield a bicarbonate ion and a hydrogen ion.
° The chemical equilibrium between carbonic acid and bicarbonate acts as a pH regulator. The equilibrium shifts left or right as other metabolic processes add or remove H+ from the solution.
Acid precipitation threatens the fitness of the environment.
· Acid precipitation is a serious assault on water quality in some industrialized areas.
° Uncontaminated rain has a slightly acidic pH of 5.6.
° The acid is a product of the formation of carbonic acid from carbon dioxide and water.
· Acid precipitation occurs when rain, snow, or fog has a pH that is more acidic than 5.6.
· Acid precipitation is caused primarily by sulfur oxides and nitrogen oxides in the atmosphere.
° These molecules react with water to form strong acids that fall to the surface with rain or snow.
· The major source of these oxides is the burning of fossil fuels (coal, oil, and gas) in factories and automobiles.
· The presence of tall smokestacks allows this pollution to spread from its site of origin to contaminate relatively pristine areas thousands of kilometers away.
° In 2001, rain in the Adirondack Mountains of upstate New York had an average pH of 4.3.
· The effects of acids in lakes and streams are more pronounced in the spring during snowmelt.
° As the surface snows melt and drain down through the snowfield, the meltwater accumulates acid and brings it into lakes and streams all at once.
° The pH of early meltwater may be as low as 3.
· Acid precipitation has a great impact on the eggs and the early developmental stages of aquatic organisms that are abundant in the spring.
· Thus, strong acidity can alter the structure of molecules and impact ecological communities.
· Direct impacts of acid precipitation on forests and terrestrial life are more controversial.
· However, acid precipitation can impact soils by affecting the solubility of soil minerals.
° Acid precipitation can wash away key soil buffers and plant nutrients such as calcium and magnesium ions.
° It can also increase the concentrations of compounds such as aluminum to toxic levels.
° This has done major damage to forests in Europe and substantial damage of forests in North America.
° Progress has been made in reducing acid precipitation.

Chapter 2 – The Chemical Context of Life – Lecture Outline

Chapter 2 The Chemical Context of Life Lecture Outline

Overview: Chemical Foundations of Biology

Living organisms and the world they live in are subject to the basic laws of physics and chemistry.
Biology is a multidisciplinary science, drawing on insights from other sciences.
Life can be organized into a hierarchy of structural levels.
At each successive level, additional emergent properties appear.

Concept 2.1 Matter consists of chemical elements in pure form and in combinations called compounds

Organisms are composed of matter.
Matter is anything that takes up space and has mass.
Matter is made up of elements.
An element is a substance that cannot be broken down into other substances by chemical reactions.
There are 92 naturally occurring elements.
Each element has a unique symbol, usually the first one or two letters of the name. Some of the symbols are derived from Latin or German names.
A compound is a substance consisting of two or more elements in a fixed ratio.
Table salt (sodium chloride or NaCl) is a compound with equal numbers of atoms of the elements chlorine and sodium.
While pure sodium is a metal and chlorine is a gas, they combine to form an edible compound. This change in characteristics when elements combine to form a compound is an example of an emergent property.
25 chemical elements are essential to life.
About 25 of the 92 natural elements are known to be essential for life.
Four elements—carbon (C), oxygen (O), hydrogen (H), and nitrogen (N)—make up 96% of living matter.
Most of the remaining 4% of an organism’s weight consists of phosphorus (P), sulfur (S), calcium (Ca), and potassium (K).
Trace elements are required by an organism but only in minute quantities.
Some trace elements, like iron (Fe), are required by all organisms.
Other trace elements are required by only some species.
For example, a daily intake of 0.15 milligrams of iodine is required for normal activity of the human thyroid gland.

Concept 2.2 An element’s properties depend on the structure of its atoms

Each element consists of unique atoms.
An atom is the smallest unit of matter that still retains the properties of an element.
Atoms are composed of even smaller parts, called subatomic particles.
Two of these, neutrons and protons, are packed together to form a dense core, the atomic nucleus, at the center of an atom.
Electrons can be visualized as forming a cloud of negative charge around the nucleus.
Each electron has one unit of negative charge.
Each proton has one unit of positive charge.
Neutrons are electrically neutral.
The attractions between the positive charges in the nucleus and the negative charges of the electrons keep the electrons in the vicinity of the nucleus.
A neutron and a proton are almost identical in mass, about 1.7 × 10−24 gram per particle.
For convenience, a smaller unit of measure, the dalton, is used to measure the mass of subatomic particles, atoms, or molecules.
The mass of a neutron or a proton is close to 1 dalton.
The mass of an electron is about 1/2000 that of a neutron or proton.
Therefore, we typically ignore the contribution of electrons when determining the total mass of an atom.
All atoms of a particular element have the same number of protons in their nuclei.
This number of protons is the element’s unique atomic number.
The atomic number is written as a subscript before the symbol for the element. For example, 2He means that an atom of helium has 2 protons in its nucleus.
Unless otherwise indicated, atoms have equal numbers of protons and electrons and, therefore, no net charge.
Therefore, the atomic number tells us the number of protons and the number of electrons that are found in a neutral atom of a specific element.
The mass number is the sum of the number of protons and neutrons in the nucleus of an atom.
Therefore, we can determine the number of neutrons in an atom by subtracting the number of protons (the atomic number) from the mass number.
The mass number is written as a superscript before an element’s symbol (for example, 4He).
The atomic weight of an atom, a measure of its mass, can be approximated by the mass number.
For example, 4He has a mass number of 4 and an estimated atomic weight of 4 daltons. More precisely, its atomic weight is 4.003 daltons.
While all atoms of a given element have the same number of protons, they may differ in the number of neutrons.
Two atoms of the same element that differ in the number of neutrons are called isotopes.
In nature, an element occurs as a mixture of isotopes.
For example, 99% of carbon atoms have 6 neutrons (12C).
Most of the remaining 1% of carbon atoms have 7 neutrons (13C) while the rarest carbon isotope, with 8 neutrons, is 14C.
Most isotopes are stable; they do not tend to lose particles.
Both 12C and 13C are stable isotopes.
The nuclei of some isotopes are unstable and decay spontaneously, emitting particles and energy.
14C is one of these unstable isotopes, or radioactive isotopes.
When 14C decays, one of its neutrons is converted to a proton and an electron.
This converts 14C to 14N, transforming the atom to a different element.
Radioactive isotopes have many applications in biological research.
Radioactive decay rates can be used to date fossils.
Radioactive isotopes can be used to trace atoms through metabolic processes.
Radioactive isotopes are also used to diagnose medical disorders.
For example, a known quantity of a substance labeled with a radioactive isotope can be injected into the blood, and its rate of excretion in the urine can be measured.
Also, radioactive tracers can be used with imaging instruments to monitor chemical processes in the body.
While useful in research and medicine, the energy emitted in radioactive decay is hazardous to life.
This energy can destroy molecules within living cells.
The severity of damage depends on the type and amount of radiation that the organism absorbs.
Electron configuration influences the chemical behavior of an atom.
Simplified models of the atom greatly distort the atom’s relative dimensions.
To gain an accurate perspective of the relative proportions of an atom, if the nucleus was the size of a golf ball, the electrons would be moving about 1 kilometer from the nucleus.
Atoms are mostly empty space.
When two elements interact during a chemical reaction, it is actually their electrons that are involved.
The nuclei do not come close enough to interact.
The electrons of an atom vary in the amount of energy they possess.
Energy is the ability to do work.
Potential energy is the energy that matter stores because of its position or location.
Water stored behind a dam has potential energy that can be used to do work turning electric generators.
Because potential energy has been expended, the water stores less energy at the bottom of the dam than it did in the reservoir.
Electrons have potential energy because of their position relative to the nucleus.
The negatively charged electrons are attracted to the positively charged nucleus.
The farther electrons are from the nucleus, the more potential energy they have.
Changes in an electron’s potential energy can only occur in steps of a fixed amount, moving the electron to a fixed location relative to the nucleus.
An electron cannot exist between these fixed locations.
The different states of potential energy that the electrons of an atom can have are called energy levels or electron shells.
The first shell, closest to the nucleus, has the lowest potential energy.
Electrons in outer shells have more potential energy.
Electrons can change their position only if they absorb or release a quantity of energy that matches the difference in potential energy between the two levels.
The chemical behavior of an atom is determined by its electron configuration—the distribution of electrons in its electron shells.
The first 18 elements, including those most important in biological processes, can be arranged in 8 columns and 3 rows.
Elements in the same row fill the same shells with electrons.
Moving from left to right, each element adds one electron (and proton) from the element before.
The first electron shell can hold only 2 electrons.
The two electrons of helium fill the first shell.
Atoms with more than two electrons must place the extra electrons in higher shells.
For example, lithium, with three electrons, has two in the first shell and one in the second shell.
The second shell can hold up to 8 electrons.
Neon, with 10 total electrons, has two in the first shell and eight in the second, filling both shells.
The chemical behavior of an atom depends mostly on the number of electrons in its outermost shell, the valence shell.
Electrons in the valence shell are known as valence electrons.
Lithium has one valence electron; neon has eight.
Atoms with the same number of valence electrons have similar chemical behaviors.
An atom with a completed valence shell, like neon, is nonreactive.
All other atoms are chemically reactive because they have incomplete valence shells.
The paths of electrons are often portrayed as concentric paths, like planets orbiting the sun.
In reality, an electron occupies a more complex three-dimensional space, an orbital.
The orbital represents the space in which the electron is found 90% of the time.
Each orbital can hold a maximum of two electrons.
The first shell has room for a single spherical 1s orbital for its pair of electrons.
The second shell can pack pairs of electrons into a spherical 2s orbital and three dumbbell-shaped 2p orbitals.
The reactivity of atoms arises from the presence of unpaired electrons in one or more orbitals of their valence shells.
Electrons occupy separate orbitals within the valence shell until forced to share orbitals.
The four valence electrons of carbon each occupy separate orbitals, but the five valence electrons of nitrogen are distributed into three unshared orbitals and one shared orbital.
When atoms interact to complete their valence shells, it is the unpaired electrons that are involved.

Concept 2.3 The formation and function of molecules depend on chemical bonding between atoms

Atoms with incomplete valence shells can interact with each other by sharing or transferring valence electrons.
These interactions typically result in the atoms remaining close together, held by attractions called chemical bonds.
The strongest chemical bonds are covalent bonds and ionic bonds.
A covalent bond is formed by the sharing of a pair of valence electrons by two atoms.
If two atoms come close enough that their unshared orbitals overlap, they will share their newly paired electrons. Each atom can count both electrons toward its goal of filling the valence shell.
For example, if two hydrogen atoms come close enough that their 1s orbitals overlap, then they can share a pair of electrons, with each atom contributing one.
Two or more atoms held together by covalent bonds constitute a molecule.
We can abbreviate the structure of the molecule by substituting a line for each pair of shared electrons, drawing the structural formula.
H—H is the structural formula for the covalent bond between two hydrogen atoms.
The molecular formula indicates the number and types of atoms present in a single molecule.
H2 is the molecular formula for hydrogen gas.
Oxygen needs to add 2 electrons to the 6 already present to complete its valence shell.
Two oxygen atoms can form a molecule by sharing two pairs of valence electrons.
These atoms have formed a double covalent bond.
Every atom has a characteristic total number of covalent bonds that it can form, equal to the number of unpaired electrons in the outermost shell. This bonding capacity is called the atom’s valence.
The valence of hydrogen is 1.
Oxygen is 2.
Nitrogen is 3.
Carbon is 4.
Phosphorus should have a valence of 3, based on its three unpaired electrons, but in biological molecules it generally has a valence of 5, forming three single covalent bonds and one double bond.
Covalent bonds can form between atoms of the same element or atoms of different elements.
While both types are molecules, the latter are also compounds.
Water, H2O, is a compound in which two hydrogen atoms form single covalent bonds with an oxygen atom.
This satisfies the valences of both elements.
Methane, CH4, satisfies the valences of both C and H.
The attraction of an atom for the shared electrons of a covalent bond is called its electronegativity.
Strongly electronegative atoms attempt to pull the shared electrons toward themselves.
If electrons in a covalent bond are shared equally, then this is a nonpolar covalent bond.
A covalent bond between two atoms of the same element is always nonpolar.
A covalent bond between atoms that have similar electronegativities is also nonpolar.
Because carbon and hydrogen do not differ greatly in electronegativities, the bonds of CH4 are nonpolar.
When two atoms that differ in electronegativity bond, they do not share the electron pair equally and form a polar covalent bond.
The bonds between oxygen and hydrogen in water are polar covalent because oxygen has a much higher electronegativity than does hydrogen.
Compounds with a polar covalent bond have regions of partial negative charge near the strongly electronegative atom and regions of partial positive charge near the weakly electronegative atom.
An ionic bond can form if two atoms are so unequal in their attraction for valence electrons that one atom strips an electron completely from the other.
For example, sodium, with one valence electron in its third shell, transfers this electron to chlorine, with 7 valence electrons in its third shell.
Now, sodium has a full valence shell (the second) and chlorine has a full valence shell (the third).
After the transfer, both atoms are no longer neutral, but have charges and are called ions.
Sodium has one more proton than electrons and has a net positive charge.
Atoms with positive charges are cations.
Chlorine has one more electron than protons and has a net negative charge.
Atoms with negative charges are anions.
Because of differences in charge, cations and anions are attracted to each other to form an ionic bond.
Atoms in an ionic bond need not have acquired their charges by transferring electrons with each other.
Compounds formed by ionic bonds are ionic compounds, or salts. An example is NaCl, or table salt.
The formula for an ionic compound indicates the ratio of elements in a crystal of that salt. NaCl is not a molecule, but a salt crystal with equal numbers of Na+ and Cl− ions.
Ionic compounds can have ratios of elements different from 1:1.
For example, the ionic compound magnesium chloride (MgCl2) has 2 chloride atoms per magnesium atom.
Magnesium needs to lose 2 electrons to drop to a full outer shell; each chlorine atom needs to gain 1.
Entire molecules that have full electrical charges are also called ions.
In the salt ammonium chloride (NH4Cl), the anion is Cl− and the cation is NH4+.
The strength of ionic bonds depends on environmental conditions, such as moisture.
Water can dissolve salts by reducing the attraction between the salt’s anions and cations.
Weak chemical bonds play important roles in the chemistry of life.
Within a cell, weak, brief bonds between molecules are important to a variety of processes.
For example, signal molecules from one neuron use weak bonds to bind briefly to receptor molecules on the surface of a receiving neuron.
This triggers a response by the recipient.
Weak interactions include ionic bonds (weak in water), hydrogen bonds, and van der Waals interactions.
Hydrogen bonds form when a hydrogen atom already covalently bonded to a strongly electronegative atom is attracted to another strongly electronegative atom.
These strongly electronegative atoms are typically nitrogen or oxygen.
These bonds form because a polar covalent bond leaves the hydrogen atom with a partial positive charge and the other atom with a partial negative charge.
The partially positive–charged hydrogen atom is attracted to regions of full or partial negative charge on molecules, atoms, or even regions of the same large molecule.
For example, ammonia molecules and water molecules interact with weak hydrogen bonds.
In the ammonia molecule, the hydrogen atoms have partial positive charges, and the more electronegative nitrogen atom has a partial negative charge.
In the water molecule, the hydrogen atoms also have partial positive charges, and the oxygen atom has a partial negative charge.
Areas with opposite charges are attracted.
Even molecules with nonpolar covalent bonds can have temporary regions of partial negative and positive charge.
Because electrons are constantly in motion, there can be periods when they accumulate by chance in one area of a molecule.
This creates ever-changing regions of partial negative and positive charge within a molecule.
Molecules or atoms in close proximity can be attracted by these fleeting charge differences, creating van der Waals interactions.
While individual bonds (ionic, hydrogen, van der Waals) are weak and temporary, collectively they are strong and play important biological roles.
A molecule’s biological function is related to its shape.
The three-dimensional shape of a molecule is an important determinant of its function in a cell.
A molecule with two atoms is always linear.
However, a molecule with more than two atoms has a more complex shape.
The shape of a molecule is determined by the positions of the electron orbitals that are shared by the atoms involved in the bond.
When covalent bonds form, the orbitals in the valence shell of each atom rearrange.
For atoms with electrons in both s and p orbitals, the formation of a covalent bonds leads to hybridization of the orbitals to four new orbitals in a tetrahedral shape.
In a water molecule, two of oxygen’s four hybrid orbitals are shared with hydrogen atoms. The water molecule is shaped like a V, with its two covalent bonds spread apart at an angle of 104.5°.
In a methane molecule (CH4), the carbon atom shares all four of its hybrid orbitals with H atoms. The carbon nucleus is at the center of the tetrahedron, with hydrogen nuclei at the four corners.
Large organic molecules contain many carbon atoms. In these molecules, the tetrahedral shape of carbon bonded to four other atoms is often a repeating motif.
Biological molecules recognize and interact with one another with a specificity based on molecular shape.
For example, signal molecules from a transmitting cell have specific shapes that bind to complementary receptor molecules on the surface of the receiving cell.
The temporary attachment of the receptor and signal molecule stimulates activity in the receptor cell.
Molecules with similar shapes can have similar biological effects.
For example, morphine, heroin, and other opiate drugs are similar enough in shape that they can bind to the same receptors as natural signal molecules called endorphins.
Binding of endorphins to receptors on brain cells produces euphoria and relieves pain. Opiates mimic these natural endorphin effects.

Concept 2.4 Chemical reactions make and break chemical bonds

In chemical reactions, chemical bonds are broken and reformed, leading to new arrangements of atoms.
The starting molecules in the process are called reactants, and the final molecules are called products.
In a chemical reaction, all of the atoms in the reactants must be present in the products.
The reactions must be “balanced”.
Matter is conserved in a chemical reaction.
Chemical reactions rearrange matter; they do not create or destroy matter.
For example, we can recombine the covalent bonds of H2 and O2 to form the new bonds of H2O.
In this reaction, two molecules of H2 combine with one molecule of O2 to form two molecules of H2O.
Photosynthesis is an important chemical reaction.
Humans and other animals ultimately depend on photosynthesis for food and oxygen.
Green plants combine carbon dioxide (CO2) from the air and water (H2O) from the soil to create sugar molecules and release molecular oxygen (O2) as a by-product.
This chemical reaction is powered by sunlight.
The overall process of photosynthesis is 6CO2 + 6H2O –> C6H12O6 + 6O2.
This process occurs in a sequence of individual chemical reactions that rearrange the atoms of the reactants to form the products.
Some chemical reactions go to completion; that is, all the reactants are converted to products.
Most chemical reactions are reversible, with the products in the forward reaction becoming the reactants for the reverse reaction.
For example in this reaction: 3H2 + N2 <=> 2NH3 hydrogen and nitrogen molecules combine to form ammonia, but ammonia can decompose to hydrogen and nitrogen molecules.
Initially, when reactant concentrations are high, they frequently collide to create products.
As products accumulate, they collide to reform reactants.
Eventually, the rate of formation of products is the same as the rate of breakdown of products (formation of reactants), and the system is at chemical equilibrium.
At equilibrium, products and reactants are continually being formed, but there is no net change in the concentrations of reactants and products.
At equilibrium, the concentrations of reactants and products are typically not equal, but their concentrations have stabilized at a particular ratio.

Chapter 3 – Water Objectives

Chapter 3 Water & the Fitness of the Environment
Objectives
The Properties of Water 1. With the use of a diagram or diagrams, explain why water molecules are: a. polar b. capable of hydrogen bonding with four neighboring water molecules 2. List four characteristics of water that are emergent properties resulting from hydrogen bonding. 3. Define cohesion and adhesion. Explain how water’s cohesion and adhesion contribute to the movement of water from the roots to the leaves of a tree. 4. Distinguish between heat and temperature, using examples to clarify your definitions. 5. Explain the following observations by referring to the properties of water: n Coastal areas have milder climates than adjacent inland areas. n Ocean temperatures fluctuate much less than air temperatures on land. n Insects like water striders can walk on the surface of a pond without breaking the surface. n If you slightly overfill a water glass, the water will form a convex surface above the top of the glass. n If you place a paper towel so that it touches spilled water, the towel will draw in the water. n Ice floats on water. n Humans sweat and dogs pant to cool themselves on hot days. 6. Distinguish among a solute, a solvent, and a solution. 7. Distinguish between hydrophobic and hydrophilic substances. 8. Explain how you would make up a one molar (1M) solution of ethyl alcohol. The Dissociation of Water Molecules 9. Name the products of the dissociation of water and give their concentration in pure water. 10. Define acid, base, and pH. 11. Explain how acids and bases may directly or indirectly alter the hydrogen ion concentration of a solution. 12. Using the bicarbonate buffer system as an example, explain how buffers work. 13. Briefly explain the causes and effects of acid precipitation.
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Chapter 2 Chemical Context of Life Objectives

Chapter 2 Chemical Context of Life
Objectives
Elements and Compounds Distinguish between an element and a compound. Identify the four elements that make up 96% of living matter. Define the term trace element and give an example. Atoms and Molecules Draw and label a simplified model of an atom. Explain how this model simplifies our understanding of atomic structure. Distinguish between each of the following pairs of terms: neutron and proton atomic number and mass number atomic weight and mass number Explain how the atomic number and mass number of an atom can be used to determine the number of neutrons. Explain how two isotopes of an element are similar. Explain how they are different. Describe two biological applications that use radioactive isotopes. Define the terms energy and potential energy. Explain why electrons in the first electron shell have less potential energy than electrons in higher electron shells. Distinguish among nonpolar covalent, polar covalent and ionic bonds. Explain why strong covalent bonds and weak bonds are both essential in living organisms. Distinguish between hydrogen bonds and van der Waals interactions. Give an example that illustrates how a molecule’s shape can determine its biological function. Explain what is meant by a chemical equilibrium.
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Elements and Compounds